The army says it has killed around 60 fighters, while five soldiers were also killed within the first 24 hours of the offensive.
But no independent verificiation of casualities has yet been made. Foreign journalists are barred from the war zone and many Pakistani reporters have left the region.
Around 28,000 soldiers have been deployed to battle a Taliban that Islamabad estimates to be about 10,000 strong, including a thousand Uzbek fighters and some Arab al-Qaeda members.
The army had launched brief offensives in South Waziristan before, the first in 2004 when it suffered heavy casualties before striking a peace deal.
But Pakistan analysts say there was never any chance of a renegotiated peace settlement.
In an interview with Al Jazeera on Monday, political analyst Ishtiaq Ahmed said "the time for deals is over".
"The security establishment as well as the civilian government are absolutley clear that they will not negotiate with the Pakistan Taliban or its terrorist affiliates across the country", Ahmed said.
"There are rifts in the Taliban movement and there are people in North Waziristan who have openly condemned terrorist attacks within Pakistan. It seems the government is trying to cultivate their support", he said.
The latest offensive could be its toughest test and the army will be attempting to prevent Taliban factions in Afghanistan from staying out of the fight.
About 100,000 civilians have fled South Waziristan in anticipation of the offensive, with some 16,000 coming out in the last few days, the army said.
But the exodus is not expected to bring a humanitarian crisis similar to one this year when about 2 million people fled from an offensive in the Swat valley, northwest of Islamabad.
South Waziristan's population is about 500,000, according to the latest figures, and many residents have houses on government-controlled lowland to the east. People traditionally head up to Waziristan in the summer with their flocks and back to the lowland in the autumn.
Most of the displaced who do not have houses on the lowland are staying with friends and relatives, officials said.
The new offensive has prompted the authorities to close down for a week a majority of military schools and colleges across Pakistan.
The decision was announced on Sunday after Taliban threatened that a school bus may be hijacked, security officials said.
A number of private and government schools were also considering a temporary closure, Pakistani security officials said.
Al Jazeera's Alan Fisher, reporting from the Pakistani capital, Islamabad, said government officials feared that schools could be targeted by suicide bombers, or that pupils could be taken hostage by those threatening to blow the school up.
"We have no way of confirming whether or not the threats were made by the Taliban, but the threat was enough for the Pakistani government to take this action," he said.